Back to Dev & increase memory for full size test

CHANGELOG.md

@@ -3,6 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## dev
+
+- Increase memory for full size tests
+
+## v1.0.4 - 2024-04-21
+
+- Fixed incorrect assignment of cluster groups (Issue #131).
+
 ## v1.0.3 - 2024-02-23
 
 - Improved TPM file splitting performance (Issue #120).

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnasplice/releases/tag/1.0.3" target="_blank">nf-core/rnasplice</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnasplice/tree/dev" target="_blank">nf-core/rnasplice</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnasplice/1.0.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnasplice/dev/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-rnasplice-methods-description":

conf/test_full.config

@@ -25,3 +25,10 @@ params {
     genome         = 'GRCh37'
 
 }
+
+
+process {
+    withName: 'NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
+        memory = 144.GB
+    }
+}

modules/local/suppa_clusterevents.nf

@@ -11,7 +11,7 @@ process CLUSTEREVENTS {
     input:
     tuple val(cond1), val(cond2), path(dpsi)
     tuple val(cond1), val(cond2), path(psivec)
-    val group_ranges // e.g. 1-3,4-6
+    tuple val(cond1), val(cond2), val(group_ranges) // e.g. 1-3,4-6
     val prefix
     val clusterevents_dpsithreshold    // val params.clusterevents_dpsithreshold
     val clusterevents_eps              // val params.clusterevents_eps

modules/local/suppa_clustergroups.nf

@@ -11,7 +11,7 @@ process CLUSTERGROUPS {
     tuple val(cond1), val(cond2), path(psivec)
 
     output:
-    stdout
+    tuple val(cond1), val(cond2), stdout
 
     when:
     task.ext.when == null || task.ext.when

nextflow.config

@@ -356,7 +356,7 @@ manifest {
     description     = """Alternative splicing analysis using RNA-seq."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0.3'
+    version         = 'dev'
     doi             = '10.5281/zenodo.8424632'
 }
 

subworkflows/local/suppa.nf

@@ -209,6 +209,15 @@ workflow SUPPA {
 
                 ch_groups_ioe = CLUSTERGROUPS_IOE.out
 
+                // Join channels to ensure consistent order
+
+                ch_clusterevents_ioe = ch_dpsi_local.join(ch_psivec_local, by: [0, 1]).join(ch_groups_ioe, by: [0, 1])
+
+                // Splitting the joined channel back into three separate channels
+                ch_dpsi_local = ch_clusterevents_ioe.map { it -> [it[0], it[1], it[2]] }
+                ch_psivec_local = ch_clusterevents_ioe.map { it -> [it[0], it[1], it[3]] }
+                ch_groups_ioe = ch_clusterevents_ioe.map { it -> [it[0], it[1], it[4]] }
+
                 // Run Clustering
 
                 CLUSTEREVENTS_IOE(
@@ -360,6 +369,15 @@ workflow SUPPA {
 
                 ch_groups_ioi = CLUSTERGROUPS_IOI.out
 
+                // Join channels to ensure consistent order
+
+                ch_clusterevents_ioi = ch_dpsi_isoform.join(ch_psivec_isoform, by: [0, 1]).join(ch_groups_ioi, by: [0, 1])
+
+                // Splitting the joined channel back into three separate channels
+                ch_dpsi_isoform = ch_clusterevents_ioi.map { it -> [it[0], it[1], it[2]] }
+                ch_psivec_isoform = ch_clusterevents_ioi.map { it -> [it[0], it[1], it[3]] }
+                ch_groups_ioi = ch_clusterevents_ioi.map { it -> [it[0], it[1], it[4]] }
+
                 // Run Clustering
 
                 CLUSTEREVENTS_IOI(